Align Acetate uptake permease, ActP1; also takes up tellurite (characterized)
to candidate Echvi_1267 Echvi_1267 probable sodium:solute symporter, VC_2705 subfamily
Query= TCDB::D5AU53 (551 letters) >FitnessBrowser__Cola:Echvi_1267 Length = 567 Score = 189 bits (480), Expect = 2e-52 Identities = 149/523 (28%), Positives = 237/523 (45%), Gaps = 88/523 (16%) Query: 35 WTAIAMFLFFVVATLILTGWAARRTKSTADFYTAGGGITGFQNGLAIAGDYMSAAAFLGI 94 WT I + L F + I W+ R ST +FY AGGG++ NG+A D+MSAA+F+ + Sbjct: 6 WTYILVGLSFALYIGIAI-WS--RAGSTKEFYVAGGGVSPLANGMATGADWMSAASFISM 62 Query: 95 SGMVFAKGVDGAIYTVGFTVGWPFILFLIAERLRNLGKFTFADITSFRLEQTRIRTLSAL 154 +G++ G DG++Y +G+T G+ + L+A LR GKFT D R + R ++ Sbjct: 63 AGLISFMGYDGSVYLMGWTGGYVLLALLLAPYLRKFGKFTVPDFVGDRYYSNKARVVAVF 122 Query: 155 GALTVVVFYLIAQMVGAGKLIQLLFGLPYSYAVILVGVLMVLYVTFGGMLATTWVQIVKA 214 A+ + Y+ QM G G + + + VI+ ++ Y GGM T+ Q+ + Sbjct: 123 CAIFISFTYVAGQMRGVGIVFSRYLEVDINTGVIIGMCIVFFYAVLGGMKGITYTQVAQY 182 Query: 215 VMLLSGATLLVILGLAQFGFSPERLMADALANHAKGAAILEPTPLVTDWVSGV------- 267 +L+ + I F +L ++ + G + + T L+ D + GV Sbjct: 183 CVLIFAFMVPAI-------FISMQLTSNPIPQLGLGGTVADGTYLL-DKLDGVLTDLGFH 234 Query: 268 -------------SLALALMFGPAGLPHILMRFFTVPDAKEARKSVFYATGFVAYFFVLT 314 ++ LALM G AGLPH+++RFFTVP K+AR S YA F+A + Sbjct: 235 AYTSGKKSMGDMFAITLALMVGTAGLPHVIVRFFTVPRVKDARLSAGYALVFIAILYTTA 294 Query: 315 TTIG----FLAITLVGKNP-------------------------------------EFLD 333 + + AI V + P EF Sbjct: 295 PAVSAFGIYNAIDSVSEKPIDDLPEWVTNWQQTQLIKINDKNQDGVVQYVADPERNEFTI 354 Query: 334 AKGIIGGGNMAAIHLAQAVGGNIFLGFISAVAFATILAVVSGLALSGASAVAHDLYANVV 393 K I+ N L N +G ++A A L+ +GL L +++V+ DL N Sbjct: 355 DKDIMVLANPEIAQLP-----NWVVGLVAAGGMAAALSTAAGLLLVISTSVSRDLAKNF- 408 Query: 394 KKGAAADKAEMRVSRIATLVLGVLAIVLGLMFENQNIAFMVGLAFGLAASVNFPVLLLSI 453 +DK E+ ++R+A V ++A G+ +A +V AFGLAA+ FPV+++ I Sbjct: 409 -NPGISDKKELLIARVAAAVAVIVAGYFGVN-PPGFVAEVVAFAFGLAAASFFPVIIMGI 466 Query: 454 FWKGMTTRGAFIGGLIGLVVSIVLVVLGPAVWVDVFKFDTPIF 496 F K M GA G L+GLV ++ ++ FKF T +F Sbjct: 467 FSKRMNKEGAIWGMLVGLVFTLSYII--------YFKFGTDLF 501 Lambda K H 0.328 0.140 0.414 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 814 Number of extensions: 41 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 551 Length of database: 567 Length adjustment: 36 Effective length of query: 515 Effective length of database: 531 Effective search space: 273465 Effective search space used: 273465 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory